Acsf3 (acyl-CoA synthetase family member 3) - Rat Genome Database

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Gene: Acsf3 (acyl-CoA synthetase family member 3) Rattus norvegicus
Analyze
Symbol: Acsf3
Name: acyl-CoA synthetase family member 3
RGD ID: 1586037
Description: Predicted to have malonyl-CoA synthetase activity and very long-chain fatty acid-CoA ligase activity. Predicted to be involved in fatty acid biosynthetic process and malonate catabolic process. Predicted to localize to mitochondrion. Human ortholog(s) of this gene implicated in combined malonic and methylmalonic acidemia. Orthologous to human ACSF3 (acyl-CoA synthetase family member 3); INTERACTS WITH bisphenol A; Soman; tetrachloromethane.
Type: protein-coding
RefSeq Status: MODEL
Also known as: acyl-CoA synthetase family member 3, mitochondrial; LOC498962; malonate--CoA ligase ACSF3, mitochondrial; similar to C50H11.1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21950,835,116 - 50,875,557 (+)NCBI
Rnor_6.0 Ensembl1955,594,831 - 55,635,122 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01955,594,801 - 55,635,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01966,302,623 - 66,342,436 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,066,291 - 53,106,673 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1950,073,106 - 50,113,121 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
mitochondrion  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:17762044   PMID:18614015   PMID:21642549   PMID:21846720  


Genomics

Comparative Map Data
Acsf3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21950,835,116 - 50,875,557 (+)NCBI
Rnor_6.0 Ensembl1955,594,831 - 55,635,122 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01955,594,801 - 55,635,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01966,302,623 - 66,342,436 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,066,291 - 53,106,673 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1950,073,106 - 50,113,121 (+)NCBICelera
Cytogenetic Map19q12NCBI
ACSF3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1689,088,375 - 89,164,121 (+)EnsemblGRCh38hg38GRCh38
GRCh381689,093,847 - 89,160,556 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371689,160,260 - 89,222,641 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,687,825 - 87,749,670 (+)NCBINCBI36hg18NCBI36
Celera1674,226,564 - 74,287,794 (+)NCBI
Cytogenetic Map16q24.3NCBI
HuRef1674,859,689 - 74,921,455 (+)NCBIHuRef
CHM1_11690,571,314 - 90,633,542 (+)NCBICHM1_1
Acsf3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,502,209 - 123,544,626 (+)NCBIGRCm39mm39
GRCm39 Ensembl8123,502,225 - 123,544,619 (+)Ensembl
GRCm388122,775,470 - 122,817,887 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8122,775,486 - 122,817,880 (+)EnsemblGRCm38mm10GRCm38
MGSCv378125,299,405 - 125,341,781 (+)NCBIGRCm37mm9NCBIm37
MGSCv368125,666,626 - 125,703,971 (+)NCBImm8
Celera8127,007,875 - 127,052,230 (+)NCBICelera
Cytogenetic Map8E1NCBI
Acsf3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555412,837,448 - 2,876,316 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555412,837,487 - 2,876,220 (+)NCBIChiLan1.0ChiLan1.0
ACSF3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11689,465,691 - 89,524,210 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1689,467,997 - 89,523,825 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01669,842,709 - 69,907,075 (+)NCBIMhudiblu_PPA_v0panPan3
ACSF3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1564,288,339 - 64,338,596 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl564,289,295 - 64,414,637 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha564,304,235 - 64,354,696 (-)NCBI
ROS_Cfam_1.0564,519,689 - 64,569,550 (-)NCBI
UMICH_Zoey_3.1564,539,014 - 64,589,483 (-)NCBI
UNSW_CanFamBas_1.0564,377,020 - 64,427,451 (-)NCBI
UU_Cfam_GSD_1.0564,783,458 - 64,833,225 (-)NCBI
Acsf3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934924,946,656 - 24,983,470 (-)NCBI
SpeTri2.0NW_004936641700,218 - 736,875 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ACSF3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6663,109 - 712,015 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16663,201 - 708,800 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26826,070 - 843,606 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ACSF3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1574,464,357 - 74,526,173 (+)NCBI
ChlSab1.1 Ensembl574,464,651 - 74,525,660 (+)Ensembl
Acsf3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624746627,089 - 655,922 (-)NCBI

Position Markers
RH131581  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01955,576,458 - 55,576,640NCBIRnor6.0
Rnor_5.01966,284,270 - 66,284,452UniSTSRnor5.0
RGSC_v3.41953,047,923 - 53,048,105UniSTSRGSC3.4
Celera1950,054,762 - 50,054,944UniSTS
RH 3.4 Map19705.41UniSTS
Cytogenetic Map19q12UniSTS
RH131927  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01955,634,968 - 55,635,169NCBIRnor6.0
Rnor_5.01966,342,095 - 66,342,296UniSTSRnor5.0
RGSC_v3.41953,106,328 - 53,106,529UniSTSRGSC3.4
Celera1950,112,777 - 50,112,978UniSTS
RH 3.4 Map19710.31UniSTS
Cytogenetic Map19q12UniSTS
BF401198  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01955,543,317 - 55,543,504NCBIRnor6.0
Rnor_5.01966,251,366 - 66,251,553UniSTSRnor5.0
RGSC_v3.41953,014,379 - 53,014,566UniSTSRGSC3.4
Celera1950,021,500 - 50,021,687UniSTS
RH 3.4 Map19706.81UniSTS
Cytogenetic Map19q12UniSTS
RH137904  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01955,538,062 - 55,538,274NCBIRnor6.0
Rnor_5.01966,246,082 - 66,246,294UniSTSRnor5.0
RGSC_v3.41953,009,174 - 53,009,386UniSTSRGSC3.4
Celera1950,016,788 - 50,017,000UniSTS
RH 3.4 Map19704.31UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:109
Count of miRNA genes:87
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000020313
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 17 41 3 68 35 36 11
Low 2 8 8 6 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020313   ⟹   ENSRNOP00000020313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1955,594,831 - 55,635,122 (+)Ensembl
RefSeq Acc Id: XM_001079424   ⟹   XP_001079424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1950,073,106 - 50,113,121 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772665   ⟹   XP_008770887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,835,131 - 50,875,557 (+)NCBI
Rnor_6.01955,594,802 - 55,635,312 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008774254   ⟹   XP_008772476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1950,073,107 - 50,113,121 (+)NCBI
Sequence:
RefSeq Acc Id: XM_574249   ⟹   XP_574249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,835,116 - 50,875,557 (+)NCBI
Rnor_6.01955,594,801 - 55,635,312 (+)NCBI
Rnor_5.01966,302,623 - 66,342,436 (+)NCBI
RGSC_v3.41953,066,291 - 53,106,673 (+)RGD
Sequence:
RefSeq Acc Id: XR_005497077
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,835,116 - 50,861,861 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008770887 (Get FASTA)   NCBI Sequence Viewer  
  XP_574249 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92769 (Get FASTA)   NCBI Sequence Viewer  
  EDL92770 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001079424   ⟸   XM_001079424
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_574249   ⟸   XM_574249
- Peptide Label: isoform X1
- UniProtKB: D3ZUX7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008772476   ⟸   XM_008774254
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008770887   ⟸   XM_008772665
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000020313   ⟸   ENSRNOT00000020313
Protein Domains
AMP-binding   AMP-binding_C

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701225
Promoter ID:EPDNEW_R11738
Type:initiation region
Name:Acsf3_1
Description:acyl-CoA synthetase family member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01955,594,823 - 55,594,883EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1586037 AgrOrtholog
Ensembl Genes ENSRNOG00000015077 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020313 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020313 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.12780 UniProtKB/TrEMBL
InterPro AMP-bd_C UniProtKB/TrEMBL
  AMP-binding_CS UniProtKB/TrEMBL
  AMP-dep_Synth/Lig UniProtKB/TrEMBL
  AMP-dep_Synthh-like_sf UniProtKB/TrEMBL
KEGG Report rno:498962 UniProtKB/TrEMBL
NCBI Gene 498962 ENTREZGENE
Pfam AMP-binding UniProtKB/TrEMBL
  AMP-binding_C UniProtKB/TrEMBL
PhenoGen Acsf3 PhenoGen
PROSITE AMP_BINDING UniProtKB/TrEMBL
UniProt D3ZUX7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Acsf3  acyl-CoA synthetase family member 3  LOC498962  similar to C50H11.1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC498962  similar to C50H11.1      Symbol and Name status set to provisional 70820 PROVISIONAL